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Cryo-EM structure of CAK modified by covalent inhibitor SY-1365
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8ORM
Sample CDK-activating kinase
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 56288 Reported Resolution (Å) 2.4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (8ORM) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 70
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 400 Maximum Defocus (nm) 1700 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification 245614 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC v3.3.1 IMAGE ACQUISITION EPU CTF CORRECTION RELION 4.0 beta CTF CORRECTION cryoSPARC v3.3.1 MODEL FITTING UCSF ChimeraX 1.2.5 INITIAL EULER ASSIGNMENT RELION 4.0 beta FINAL EULER ASSIGNMENT RELION 4.0 beta CLASSIFICATION RELION 4.0 beta RECONSTRUCTION RELION 4.0 beta MODEL REFINEMENT PHENIX 1.20.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION